MolNFT v1 · #78840 · protein
Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10D
3SL5 · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10D”. X-ray diffraction, 2 ligands (J25, ZN), 13 pockets (best druggability 0.81). MolNFT v1 #78840 on…
- PDB
- 3SL5
- Type
- protein
- Length
- 1,302 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- J25, ZN
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 328 | 67% helix, 1% strand | Q08499 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 325 | 67% helix, 1% strand | Q08499 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 325 | 68% helix, 1% strand | Q08499 |
| D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) | protein | 324 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- J25 · diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.81 | 0.89 | 63 | EDO |
| 2 | 652 | 0.79 | 0.84 | 59 | EDO |
| 3 | 263 | 0.77 | 0.90 | 48 | empty |
| 4 | 235 | 0.76 | 0.90 | 43 | empty |
| 5 | 448 | 0.73 | 0.82 | 42 | ZN, J25 |
Interfaces
6 interfaces between chains.
- A–C · 959 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 938 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 688 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 679 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 238 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3SL5 · Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q08499
- Elsewhere: RCSB PDB 3SL5 · PDBe 3SL5 · UniProt Q08499
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